3LIT

The crystal structure of htlv protease complexed with the inhibitor KNI-10681


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B7F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.229317% PEG8000 16% PEG300, 0.2M KH2PO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8757.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.282α = 90
b = 78.282β = 90
c = 163.321γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.195094.50.1315.55.915113-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2864.70.242.71.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2B7F2.19501461546794.460.204050.20230.2622RANDOM40.833
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.52-0.76-1.522.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.684
r_dihedral_angle_3_deg19.3
r_dihedral_angle_4_deg11.579
r_scangle_it9.265
r_mcangle_it7.394
r_scbond_it7.183
r_dihedral_angle_1_deg6.741
r_mcbond_it6.085
r_angle_refined_deg1.651
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.684
r_dihedral_angle_3_deg19.3
r_dihedral_angle_4_deg11.579
r_scangle_it9.265
r_mcangle_it7.394
r_scbond_it7.183
r_dihedral_angle_1_deg6.741
r_mcbond_it6.085
r_angle_refined_deg1.651
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1766
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms46

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling